Unravelling the Importance of Transposable Elements for Phenotypic Divergence in Triploid Asexual Dandelions

Triploid dandelions arise through apomixis which is defined as the asexual formation of a seed from maternal tissues, circumventing normal meiosis and fertilization process. This form of asexuality is relatively prevalent in higher plants. However, just like other forms of asexual reproduction, apomixis is thought to have limited evolutionary potential leading apomicts to early extinction. Mutations, transposable elements (TEs) and other repetitive DNA can accumulate in non-recombining genomic regions. Nonetheless, TE dynamics may be particularly relevant within asexual lineages. While most transpositions are deleterious, increasing evidence is hinting at TE-induced mutations with potentially beneficial gene regulatory effects in non-recombining genomes. Thus far, limited evidence corroborates the accumulation of TEs in asexually reproducing organisms. This is likely due to contrasting effects of asexual reproduction on TE dynamics. Indeed, in the short term, transposition may be increased because epigenetic silencing mechanisms can be compromised following ploidy change and hybridization often accompanying transition from sexual to apomictic reproduction. In the long term conversely, clonal lineage selection may maintain benign TEs with low transposition rates.

To gain better insight into TE dynamics under apomixis, we use the model system Taraxacum officinale. Triploid apomicts (2n=3x=24) are derived from sexual diploid ancestors (2n=2x=16) established in South Central Europe. This process has led to numerous independent widespread apomictic lineages that are colonizing Northern latitudes. In previous studies, we observed transcription divergence driven mainly by TEs and TE-related genes within these triploid apomictic lineages; and detected heritable methylation variation within and between lineages. In this new study, we used low coverage Illumina genomic sequencing to compare TE content and dynamics within and between four sexual populations from France and Czech Republic against seven apomict populations sampled around eastern Europe and Sweden. We described limited TE accumulation in asexuals but a highly dynamic and variable TE compartment within apomict lineages. Additionally, focusing on one specific asexual lineage exhibiting variation in flowering time, we looked at the potential effect of new TE insertions within two candidate genes of the flowering pathway.

While we explore the dynamic of transposable elements following hybridization and change of ploidy levels in triploid apomict genomes, we propose hypotheses as how TEs can trigger additional genetic variation in young apomict lineages. We also discuss the ecological relevance of TEs in contributing to adaptive potential of natural populations facing changing environments.